Gut metagenomes of dairy workers and community controls, US
Shotgun metagenomic sequencing of 16 adult gut samples from dairy farm workers and community controls in the United States, comparing microbiome taxonomy, diversity, and antibiotic resistance gene prevalence. machine-written summary
16 samples · 16 runs · US · Age unknown · 2023 · 7.14 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 44 sample values (collection date, country, health condition, health condition detail) |
| ✓ Abstract / description | 16 sample values (location region) |
| ✓ Full text | 16 sample values (subject id) · PMC11626760 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 16 | 100% | ||||
| country | 16 | 100% | 16 | |||
| health_condition | 6 | 38% | 6 | |||
| subject_id | 16 | 100% | 16 | |||
| collection_date | 16 | 100% | 16 | |||
| detailed_location | 16 | 100% | ||||
| location_region | 16 | 100% | 16 | |||
| health_condition_detail | 6 | 38% | 6 |
- A cross-sectional comparison of gut metagenomes between dairy workers and community controls. 2024 PMID 39033279 PMC11626760 cites_accession
Archive description
<![CDATA[The project is interested in characterizing the microbiome and resistome of dairy workers,</p><p>whose exposure to the livestock farming environment places them at risk for</p><p>facilitating community transmission of antibiotic resistant genes and emerging</p><p>zoonotic diseases. Using shotgun metagenomics sequencing, we investigated differences in the taxonomy,</p><p>diversity and gene presence of the human gut microbiome of 10 dairy farm</p><p>workers and 6 community controls, with a focus on antibiotic resistance genes</p><p>and virulence factors in the occupationally-exposed cohort.]]>
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “human gut microbiome of 10 dairy farm”
- life stage study.description · “dairy farm workers and 6 community controls”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN35024728 | collection_date | 2018-02-15 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2018-02-15 |
| SAMN35024728 | country | US | R1 | 0.85 | biosample.attribute:geo_loc_name | geo_loc_name: USA: Yakima Valley, WA |
| SAMN35024728 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:title | C02-S104 |
| SAMN35024728 | health_condition_detail | C02-S104 | R1 | 0.70 | sample.name_rule:title | C02-S104 |
| SAMN35024728 | location_region | United States | R4 | 0.50 | paper.abstract | a cohort of dairy workers in the United States |
| SAMN35024728 | subject_id | SAMN35024728 | R3 | 0.75 | design.one_sample_per_subject:fulltext | 16 fecal samples (the maximum possible with budget constraints) taken from the Healthy Dairy Worker study cohort. These samples came from 10 dairy workers and |
Sequencing
16 runs over 16 samples · mean 7.33 Gbp per run (median 7.14 Gbp, total 117.31 Gbp; 16 runs with a base count) · layout PAIRED 16 · platform ILLUMINA 16 · models Illumina HiSeq 2500 (16) · 0% of runs with a Sandpiper profile · first public 2023-06-22 – 2023-06-23
Authors (0)
No author record.
Downloads
PRJNA971196.csv.gz (1.3 KB) · parquet (70.1 KB) — all 16 samples, every field with route and confidence · PRJNA971196_determinations.csv.gz (1.5 KB) — 76 evidence rows